reinit the tree, so we can have metadata

4 files changed, 82 insertions, 0 deletions

diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest
new file mode 100644
index 000000000000..90a0b4fd4154
--- /dev/null
+++ b/sci-biology/exonerate/Manifest
@@ -0,0 +1,6 @@
+AUX exonerate-2.2.0-asneeded.patch 362 SHA256 6c3d42a87646760cfede57c38227d379c24a7a1cc867a619667e187680757a98 SHA512 7c08fe7ee520ab7198557f5ac7f99f0bae53da77d46949d6bac78a3330fc9023a4aece085e060ad6a40303475999654dcfe5311d3a78f1d1be0d461cefbfcfb0 WHIRLPOOL f136a885fe1d50ec182d855f05a832a25451212bf4047761f76bba4435d9d3b5a47edea4bb77e9f8e082c0adac4e90d1b8537a704622e30fee285b795cd3195b
+DIST exonerate-2.2.0.tar.gz 509870 SHA256 0ea2720b1388fa329f889522f43029b416ae311f57b229129a65e779616fe5ff SHA512 c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c WHIRLPOOL dd7ba7a94b93f41d5ddbc66cc14740973dde20e875f37814229614c85312dcc1de031faab5153bc28be3284144d0f8451bd5e5115f8d9e312e4f88d771ce620c
+EBUILD exonerate-2.2.0-r2.ebuild 943 SHA256 df65037ba33c38db84e5efc46e4d4a0750aaf7ac054a378abe3d81c557ae83c7 SHA512 830ed336dd8bb4cf59fb59099d968459530fe37ae8b1874d535dadf4d3874410592d28049abbc8dd0e66ccc4e277cd7855602dcc42e7ac61394249557cf033a2 WHIRLPOOL 192f197662a28d4f56662e402a26231dd951cfe0e8172acf16686f4d2620622d239a7ff128175feb38b91bf8b49aad9f19fe7ed7a533e5bf169eaa68afb6a577
+MISC ChangeLog 2604 SHA256 837c48a04a9024668892f9dd3aa47dba377890e2ecee18a723eb0f8e3b3ca96b SHA512 2d3709081b376cd1abf2af386c2db9cb532ec1442cc5689e3c469124cb7eda7f828ba89ff22f78374581f13c52fa54518597d13367fcb977b63e91d36cd50070 WHIRLPOOL 93af106a3ff2efaa175044e78e6c0cf51d6ea52f05ad87e489f32723493956a5965e0b9a5380c2c5a9c8548e485df4b329500234fe7a1bb58b636250595b7c06
+MISC ChangeLog-2015 1396 SHA256 0f68c730203bf609473c6b2cbdf22db5657b4ebdf9c6627687db5d10d1251518 SHA512 3615e0ddbd40eea5b23937598a96c6e3affe1f28eedd4ecda6d7d4edb195819fac2fb2f84ea9c2736c7d4c07a17e9303ccd918de5b4f228bb1b03ff497c88469 WHIRLPOOL f00b2d484b5b9d5aa440eef62f95a80490e5c8c07b1cec72bda480a2515d4b3338babe2b6a323a249905d0559e23ade6880921a598f568380f83b238872afb70
+MISC metadata.xml 449 SHA256 367ce7f367d26df031c20e887300e862f50ad5bbfe0019f6dd9178267d0408f4 SHA512 ad7dce91503151adedc204bcf1b678ad8bf9bd6a0cc7a207c9225781eeb32e24906794028aba1770260a52e2a6e9c823f138a003153f3e4c49c47228bc112f49 WHIRLPOOL 873ab156b88cf810abd917a9a7e1389fcdaa98f747fc66efa038925b7431233b4255bb877ceb68d62ea84c849358132b87a464546ecdac143476dca474857cef
diff --git a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild
new file mode 100644
index 000000000000..dcd09feac3d9
--- /dev/null
+++ b/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Generic tool for pairwise sequence comparison"
+HOMEPAGE="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate"
+SRC_URI="http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos"
+IUSE="test threads utils"
+REQUIRED_USE="test? ( utils )"
+
+DEPEND="dev-libs/glib:2"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/${P}-asneeded.patch )
+
+src_prepare() {
+	default
+	sed \
+		-e 's: -O3 -finline-functions::g' \
+		-i configure.in || die
+	mv configure.{in,ac} || die
+
+	eautoreconf
+}
+
+src_configure() {
+	tc-export CC
+
+	econf \
+		--enable-glib2 \
+		--enable-largefile \
+		$(use_enable utils utilities) \
+		$(use_enable threads pthreads)
+}
+
+src_install() {
+	default
+
+	doman doc/man/man1/*.1
+}
diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch
new file mode 100644
index 000000000000..5c428979a1af
--- /dev/null
+++ b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch
@@ -0,0 +1,15 @@
+Fix build with --as-needed
+
+https://bugs.gentoo.org/268094
+
+--- a/configure.in
++++ b/configure.in
+@@ -289,7 +289,7 @@
+ if test "$enable_pthreads" = yes; then
+     echo "Using PTHREADS"
+     CFLAGS="$CFLAGS -DUSE_PTHREADS"
+-    LDFLAGS="$LDFLAGS -lpthread"
++    LIBS="$LIBS -lpthread"
+ elif test "$enable_pthreads" = no; then
+     echo "Not using pthreads"
+ else
diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml
new file mode 100644
index 000000000000..09b6a9e09e43
--- /dev/null
+++ b/sci-biology/exonerate/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <longdescription lang="en">
+		exonerate is a generic tool for pairwise sequence comparison
+	</longdescription>
+  <use>
+    <flag name="utils">Install all utilities</flag>
+  </use>
+</pkgmetadata>